2-157637588-C-A

Variant names:

• chr2-157637588-C-A
• rs2444769

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.669 in 151,808 control chromosomes in the GnomAD database, including 37,512 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (37512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101566 AN: 151688 Hom.: 37497 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.666

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.669 AC: 101598 AN: 151808 Hom.: 37512 Cov.: 30 AF XY: 0.679 AC XY: 50394 AN XY: 74192

African (AFR) AF: 0.331 AC: 13677 AN: 41342

American (AMR) AF: 0.765 AC: 11687 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2484 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4351 AN: 5160

South Asian (SAS) AF: 0.808 AC: 3888 AN: 4812

European-Finnish (FIN) AF: 0.860 AC: 9040 AN: 10512

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54013 AN: 67928

Other (OTH) AF: 0.669 AC: 1410 AN: 2108

Alfa AF: 0.774 Hom.: 24677

Bravo AF: 0.644

Asia WGS AF: 0.798 AC: 2762 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.53
PhyloP100		0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2444769; hg19: chr2-158494100;